What is proper way to wire some logic for built-in models

User is built-in model.

Where to put

models.User.on('deleted', function(id) {
 // some logic here
})

common/models/user.js is not called for built-in User model.

You can extend the built-in models to add properties, relationships, ACLs, and other model features. You can use the LoopBack model generator or do it programmatically.

Detailed steps are provided in the docs http://docs.strongloop.com/display/LB/Extending+built-in+models